Yet another Journal
In this repository we are creating a prototype for a novel biomedical journal for publishing data and analysis resources. This work was started during the Japan 2017 Biohackathon (September 2017).
Goals
Key goals the data journal are:
- Make it easy for researchers to publish data with a short paper
- Provide a review mechanism
- Make the paper citeable
- Provide usable FAIR-data mechanisms
FAIR
FAIR means the data should be
- Findable: provide useful metadata
- Accessible: provide a stable URL
- Interoperable: use common data formats
- Reproducible: provide analysis with data (at least as an example)
Technology and resources
Git
All versions of papers, review and comments are stored into a public git repository which means everything can we recovered. We will also use a database that acts as a cache of git checkouts.
RDF/OWL
Rather than rolling our own ontologies we'll use whatever is available.
WikiData and Open Citations
Wikidata/wikicite and open citations have semantic web representations which can be used to handle citations.
IPFS
To build in speed and robustness authors are encouraged to host data on the interplanetary file system (IPFS) which provides download URLs.
Programming
We opted for Python/flask for the web server. Mostly because Python has become a lingua franca in bioinformatics and Flask is a well tested and simple web development framework. For some functionalities and (perhaps) performance we will use plug-ins which can be written in any language. The REST API may be written in Elixir.
Installation
See INSTALL.md.
Development
For further reading see development docs
License
All code is published under the AGPL. See LICENSE.
Copyright
Pjotr Prins, Raoul Bonnal, Francesco Strozzi (C) 2017